In the receipt window you can set prepayment.  You enter it in the bottom right hand box and in memo I typically note the date of payment rcvd.  As invoices created you can do a deduction through receipts windows from this deposit received. 

OK, did this, however, when I make another invoice and then go to RECEIPTS to apply the prepayment, the dialogue window  is looking for a bank account number. What am I doing wrong?  Thanks

go to receipt and adjust it to the right bank account in the droop down window